public static enum SAMValidationError.Type extends java.lang.Enum<SAMValidationError.Type>
Enum Constant and Description |
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ADJACENT_INDEL_IN_CIGAR
CIGAR string contains I followed by D, or vice versa
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BAM_FILE_MISSING_TERMINATOR_BLOCK
BAM appears to be healthy, but is an older file so doesn't have terminator block.
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CIGAR_MAPS_OFF_REFERENCE
Bases corresponding to M operator in CIGAR are beyond the end of the reference.
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DUPLICATE_PROGRAM_GROUP_ID
Same program group id appears more than once
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DUPLICATE_READ_GROUP_ID
Same read group id appears more than once
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E2_BASE_EQUALS_PRIMARY_BASE
Secondary base calls should not be the same as primary, unless one or the other is N
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EMPTY_READ |
HEADER_RECORD_MISSING_REQUIRED_TAG |
HEADER_TAG_MULTIPLY_DEFINED
Header tag appears more than once in header line with different value
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INVALID_ALIGNMENT_START
alignment start is can not be correct
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INVALID_CIGAR
CIGAR string is empty for mapped read or not empty of unmapped read, or other CIGAR badness.
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INVALID_DATE_STRING
Date string is not ISO-8601
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INVALID_FLAG_FIRST_OF_PAIR
first of pair flag set for unpaired read
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INVALID_FLAG_MATE_NEG_STRAND
mate negative strand flag set for unpaired read
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INVALID_FLAG_MATE_UNMAPPED
mate unmapped flag set when mate is mapped or not set when mate is not mapped
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INVALID_FLAG_NOT_PRIM_ALIGNMENT
not primary alignment flag set for unmapped read
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INVALID_FLAG_PROPER_PAIR
proper pair flag set for unpaired read
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INVALID_FLAG_READ_UNMAPPED
mapped read flat not set for mapped read
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INVALID_FLAG_SECOND_OF_PAIR
second of pair flag set for unpaired read
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INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
supplementary alignment flag set for unmapped read
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INVALID_INDEX_FILE_POINTER
Invalid virtualFilePointer in index
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INVALID_INDEXING_BIN
Indexing bin set on SAMRecord does not agree with computed value.
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INVALID_INSERT_SIZE
inferred insert size is out of range
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INVALID_MAPPING_QUALITY
mapping quality set for unmapped read or is >= 256
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INVALID_MATE_REF_INDEX
mate reference index (MRNM) set for unpaired read
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INVALID_PLATFORM_VALUE
The read group has an invalid value set for its PL field
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INVALID_PREDICTED_MEDIAN_INSERT_SIZE
PI tag value is not numeric.
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INVALID_QUALITY_FORMAT
quality encodings out of range; appear to be Solexa or Illumina when Phread expected
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INVALID_REFERENCE_INDEX
reference index not found in sequence dictionary
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INVALID_TAG_NM
the NM tag (nucleotide differences) is incorrect
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INVALID_VERSION_NUMBER |
MATE_CIGAR_STRING_INVALID_PRESENCE
There is a Cigar String (stored in the MC Tag) for a read whose mate is NOT mapped.
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MATE_FIELD_MISMATCH
the record's mate fields do not match the corresponding fields of the mate
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MATE_NOT_FOUND
Read is marked as paired, but its pair was not found.
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MATES_ARE_SAME_END
Both mates are marked as first of pair, or both mates are marked as second of pair.
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MISMATCH_FLAG_MATE_NEG_STRAND
mate negative strand flag does not match read negative strand flag of mate
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MISMATCH_FLAG_MATE_UNMAPPED
mate unmapped flag does not match read unmapped flag of mate
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MISMATCH_MATE_ALIGNMENT_START
mate alignment does not match alignment start of mate
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MISMATCH_MATE_CIGAR_STRING
The Cigar String in the MC Tag does not match the Cigar String for the mate of this read.
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MISMATCH_MATE_REF_INDEX
mate reference index (MRNM) does not match reference index of mate
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MISMATCH_READ_LENGTH_AND_E2_LENGTH
Length of E2 (secondary base calls) and U2 (secondary base quals) tag values should match read length
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MISMATCH_READ_LENGTH_AND_QUALS_LENGTH |
MISMATCH_READ_LENGTH_AND_U2_LENGTH |
MISSING_HEADER
the sam/bam file is missing the header
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MISSING_PLATFORM_VALUE
The read group is missing its PL (platform unit) field
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MISSING_READ_GROUP
the header is missing read group information
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MISSING_SEQUENCE_DICTIONARY
there is no sequence dictionary in the header
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MISSING_TAG_NM
the NM tag (nucleotide differences) is missing
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MISSING_VERSION_NUMBER |
PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND
pair flag set but not marked as first or second of pair
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POORLY_FORMATTED_HEADER_TAG
Header tag does not have colon
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READ_GROUP_NOT_FOUND
A read group ID on a SAMRecord is not found in the header
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RECORD_MISSING_READ_GROUP
A SAMRecord is found with no read group id
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RECORD_OUT_OF_ORDER
the record is out of order
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TAG_VALUE_TOO_LARGE
Unsigned integer tag value is deprecated in BAM.
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TRUNCATED_FILE |
UNRECOGNIZED_HEADER_TYPE
Header record is not one of the standard types
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Modifier and Type | Field and Description |
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SAMValidationError.Severity |
severity |
Modifier and Type | Method and Description |
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java.lang.String |
getHistogramString() |
static SAMValidationError.Type |
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
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static SAMValidationError.Type[] |
values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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public static final SAMValidationError.Type INVALID_QUALITY_FORMAT
public static final SAMValidationError.Type INVALID_FLAG_PROPER_PAIR
public static final SAMValidationError.Type INVALID_FLAG_MATE_UNMAPPED
public static final SAMValidationError.Type MISMATCH_FLAG_MATE_UNMAPPED
public static final SAMValidationError.Type INVALID_FLAG_MATE_NEG_STRAND
public static final SAMValidationError.Type MISMATCH_FLAG_MATE_NEG_STRAND
public static final SAMValidationError.Type INVALID_FLAG_FIRST_OF_PAIR
public static final SAMValidationError.Type INVALID_FLAG_SECOND_OF_PAIR
public static final SAMValidationError.Type PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND
public static final SAMValidationError.Type INVALID_FLAG_NOT_PRIM_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT
public static final SAMValidationError.Type INVALID_FLAG_READ_UNMAPPED
public static final SAMValidationError.Type INVALID_INSERT_SIZE
SAMRecord.MAX_INSERT_SIZE
public static final SAMValidationError.Type INVALID_MAPPING_QUALITY
public static final SAMValidationError.Type INVALID_CIGAR
public static final SAMValidationError.Type ADJACENT_INDEL_IN_CIGAR
public static final SAMValidationError.Type INVALID_MATE_REF_INDEX
public static final SAMValidationError.Type MISMATCH_MATE_REF_INDEX
public static final SAMValidationError.Type INVALID_REFERENCE_INDEX
public static final SAMValidationError.Type INVALID_ALIGNMENT_START
public static final SAMValidationError.Type MISMATCH_MATE_ALIGNMENT_START
public static final SAMValidationError.Type MATE_FIELD_MISMATCH
public static final SAMValidationError.Type INVALID_TAG_NM
public static final SAMValidationError.Type MISSING_TAG_NM
public static final SAMValidationError.Type MISSING_HEADER
public static final SAMValidationError.Type MISSING_SEQUENCE_DICTIONARY
public static final SAMValidationError.Type MISSING_READ_GROUP
public static final SAMValidationError.Type RECORD_OUT_OF_ORDER
public static final SAMValidationError.Type READ_GROUP_NOT_FOUND
public static final SAMValidationError.Type RECORD_MISSING_READ_GROUP
public static final SAMValidationError.Type INVALID_INDEXING_BIN
public static final SAMValidationError.Type MISSING_VERSION_NUMBER
public static final SAMValidationError.Type INVALID_VERSION_NUMBER
public static final SAMValidationError.Type TRUNCATED_FILE
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_QUALS_LENGTH
public static final SAMValidationError.Type EMPTY_READ
public static final SAMValidationError.Type CIGAR_MAPS_OFF_REFERENCE
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_E2_LENGTH
public static final SAMValidationError.Type MISMATCH_READ_LENGTH_AND_U2_LENGTH
public static final SAMValidationError.Type E2_BASE_EQUALS_PRIMARY_BASE
public static final SAMValidationError.Type BAM_FILE_MISSING_TERMINATOR_BLOCK
public static final SAMValidationError.Type UNRECOGNIZED_HEADER_TYPE
public static final SAMValidationError.Type POORLY_FORMATTED_HEADER_TAG
public static final SAMValidationError.Type HEADER_TAG_MULTIPLY_DEFINED
public static final SAMValidationError.Type HEADER_RECORD_MISSING_REQUIRED_TAG
public static final SAMValidationError.Type INVALID_DATE_STRING
public static final SAMValidationError.Type TAG_VALUE_TOO_LARGE
public static final SAMValidationError.Type INVALID_INDEX_FILE_POINTER
public static final SAMValidationError.Type INVALID_PREDICTED_MEDIAN_INSERT_SIZE
public static final SAMValidationError.Type DUPLICATE_READ_GROUP_ID
public static final SAMValidationError.Type MISSING_PLATFORM_VALUE
public static final SAMValidationError.Type INVALID_PLATFORM_VALUE
public static final SAMValidationError.Type DUPLICATE_PROGRAM_GROUP_ID
public static final SAMValidationError.Type MATE_NOT_FOUND
public static final SAMValidationError.Type MATES_ARE_SAME_END
public static final SAMValidationError.Type MISMATCH_MATE_CIGAR_STRING
public static final SAMValidationError.Type MATE_CIGAR_STRING_INVALID_PRESENCE
public final SAMValidationError.Severity severity
public static SAMValidationError.Type[] values()
for (SAMValidationError.Type c : SAMValidationError.Type.values()) System.out.println(c);
public static SAMValidationError.Type valueOf(java.lang.String name)
name
- the name of the enum constant to be returned.java.lang.IllegalArgumentException
- if this enum type has no constant with the specified namejava.lang.NullPointerException
- if the argument is nullpublic java.lang.String getHistogramString()